mosamatic2 2.0.24__py3-none-any.whl

mosamatic2/ui/widgets/panels/tasks/applythresholdtosegmentationstaskpanel.py

@@ -0,0 +1,271 @@
+import os
+import pathlib
+import subprocess
+import sys
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QComboBox,
+    QDoubleSpinBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import ApplyThresholdToSegmentationsTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'ApplyThresholdToSegmentationsTask'
+PANEL_NAME = 'applythresholdtosegmentationstaskpanel'
+
+
+class ApplyThresholdToSegmentationsTaskPanel(TaskPanel):
+    def __init__(self):
+        super(ApplyThresholdToSegmentationsTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_button = None
+        self._segmentations_dir_line_edit = None
+        self._segmentations_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._threshold_low_spinbox = None
+        self._threshold_high_spinbox = None
+        self._label_combobox = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._open_excel_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_button:
+            self._images_dir_select_button = QPushButton('Select')
+            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_button
+    
+    def segmentations_dir_line_edit(self):
+        if not self._segmentations_dir_line_edit:
+            self._segmentations_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/segmentations_dir'))
+        return self._segmentations_dir_line_edit
+    
+    def segmentations_dir_select_button(self):
+        if not self._segmentations_dir_select_button:
+            self._segmentations_dir_select_button = QPushButton('Select')
+            self._segmentations_dir_select_button.clicked.connect(self.handle_segmentations_dir_select_button)
+        return self._segmentations_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def threshold_low_spinbox(self):
+        if not self._threshold_low_spinbox:
+            self._threshold_low_spinbox = QDoubleSpinBox(minimum=-200, maximum=150, value=5)
+            self._threshold_low_spinbox.setValue(self.settings().get_int(f'{PANEL_NAME}/threshold_low', 5))
+        return self._threshold_low_spinbox
+    
+    def threshold_high_spinbox(self):
+        if not self._threshold_high_spinbox:
+            self._threshold_high_spinbox = QDoubleSpinBox(minimum=-200, maximum=150, value=150)
+            self._threshold_high_spinbox.setValue(self.settings().get_int(f'{PANEL_NAME}/threshold_high', 150))
+        return self._threshold_high_spinbox
+    
+    def label_combobox(self):
+        if not self._label_combobox:
+            self._label_combobox = QComboBox()
+            self._label_combobox.addItems(['1', '5', '7'])
+            self._label_combobox.setCurrentText(self.settings().get(f'{PANEL_NAME}/label', '1'))
+        return self._label_combobox
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def open_excel_button(self):
+        if not self._open_excel_button:
+            self._open_excel_button = QPushButton('Open output in Excel')
+            self._open_excel_button.clicked.connect(self.handle_open_excel_button)
+        return self._open_excel_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        segmentations_dir_layout = QHBoxLayout()
+        segmentations_dir_layout.addWidget(self.segmentations_dir_line_edit())
+        segmentations_dir_layout.addWidget(self.segmentations_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Segmentations directory', segmentations_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Threshold low', self.threshold_low_spinbox())
+        self.form_layout().addRow('Threshold high', self.threshold_high_spinbox())
+        self.form_layout().addRow('Label', self.label_combobox())
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        layout.addWidget(self.open_excel_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_segmentations_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.segmentations_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = ApplyThresholdToSegmentationsTask(
+                inputs={
+                    'images': self.images_dir_line_edit().text(),
+                    'segmentations': self.segmentations_dir_line_edit().text(),
+                },
+                params={
+                    'label': int(self.label_combobox().currentText()),
+                    'threshold_low': self.threshold_low_spinbox().value(),
+                    'threshold_high': self.threshold_high_spinbox().value(),
+                },
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    def handle_open_excel_button(self):
+        file_path = os.path.join(self.output_dir_line_edit().text(), 'calculatescorestask', 'bc_scores.xlsx')
+        file_path = pathlib.Path(file_path).expanduser().resolve()
+        if not file_path.exists():
+            raise FileNotFoundError(file_path)
+        if sys.platform.startswith('win'):
+            os.startfile(str(file_path))
+        elif sys.platform == 'darwin':
+            subprocess.run(['open', str(file_path)], check=True)
+        else:
+            subprocess.run(["xdg-open", str(file_path)], check=True)
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if not os.path.isdir(self.images_dir_line_edit().text()):
+            errors.append('Images directory does not exist')
+        if self.segmentations_dir_line_edit().text() == '':
+            errors.append('Empty segmentations directory path')
+        if not os.path.isdir(self.segmentations_dir_line_edit().text()):
+            errors.append('Segmentations directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/segmentations_dir', self.segmentations_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/label', self.label_combobox().currentText())
+        self.settings().set(f'{PANEL_NAME}/threshold_low', self.threshold_low_spinbox().value())
+        self.settings().set(f'{PANEL_NAME}/threshold_high', self.threshold_high_spinbox().value())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2/ui/widgets/panels/tasks/calculatemaskstatisticstaskpanel.py

@@ -0,0 +1,215 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QSpinBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import CalculateMaskStatisticsTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'CalculateMaskStatisticsTask'
+PANEL_NAME = 'calculatemaskstatisticstaskpanel'
+
+
+class CalculateMaskStatisticsTaskPanel(TaskPanel):
+    def __init__(self):
+        super(CalculateMaskStatisticsTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._scans_dir_line_edit = None
+        self._scans_dir_select_button = None
+        self._masks_dir_line_edit = None
+        self._masks_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def scans_dir_line_edit(self):
+        if not self._scans_dir_line_edit:
+            self._scans_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/scans_dir'))
+        return self._scans_dir_line_edit
+    
+    def scans_dir_select_button(self):
+        if not self._scans_dir_select_button:
+            self._scans_dir_select_button = QPushButton('Select')
+            self._scans_dir_select_button.clicked.connect(self.handle_scans_dir_select_button)
+        return self._scans_dir_select_button
+    
+    def masks_dir_line_edit(self):
+        if not self._masks_dir_line_edit:
+            self._masks_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/masks_dir'))
+        return self._masks_dir_line_edit
+    
+    def masks_dir_select_button(self):
+        if not self._masks_dir_select_button:
+            self._masks_dir_select_button = QPushButton('Select')
+            self._masks_dir_select_button.clicked.connect(self.handle_masks_dir_select_button)
+        return self._masks_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        scans_dir_layout = QHBoxLayout()
+        scans_dir_layout.addWidget(self.scans_dir_line_edit())
+        scans_dir_layout.addWidget(self.scans_dir_select_button())
+        masks_dir_layout = QHBoxLayout()
+        masks_dir_layout.addWidget(self.masks_dir_line_edit())
+        masks_dir_layout.addWidget(self.masks_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Scans directory', scans_dir_layout)
+        self.form_layout().addRow('Masks directory', masks_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_scans_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.scans_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_masks_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.masks_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = CalculateMaskStatisticsTask(
+                inputs={
+                    'scans': self.scans_dir_line_edit().text(),
+                    'masks': self.masks_dir_line_edit().text(),
+                },
+                params=None,
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.scans_dir_line_edit().text() == '':
+            errors.append('Empty scans directory path')
+        if not os.path.isdir(self.scans_dir_line_edit().text()):
+            errors.append('Scans directory does not exist')
+        if self.masks_dir_line_edit().text() == '':
+            errors.append('Empty masks directory path')
+        if not os.path.isdir(self.masks_dir_line_edit().text()):
+            errors.append('Masks directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/scans_dir', self.scans_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/masks_dir', self.masks_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())